I can see both sides of this one...
On the one hand, get what you can get for it. It all depends on the market. I mean, it's "worth" $2500 if you can get someone to give you $2500 for it. If you have someone lined up with that much cash-in-hand, take the money. The buyer will most likely tell you (haggle) if he thinks the bike is worth less because of the master cylinder.
On the other hand, nothing makes me madder than the insane prices I see for old(er) bikes, just because they're old. Some bikes are collectible, yes, and some of the early Hondas may fall into that category. But let's face it, not every bike is collectible, and even so, how collectible (and pricey) something is tends to be pretty subjective. I think the most overused word when selling a older scoot is "rare", followed by "classic"!
Personally, I think $2500 for a less-than-perfect, non-stock, modified, 30-year-old Honda CB is...well, very much on the high side. $2500 is no small chunk of change, and if you were in the market for a bike, that sort of cash could get you newer, more reliable transportation.